1991 Mercury Marquis Alternator

I own a '91 Mercury Grand Marquis. The other night when I drove the car it sounded like something was straining under the hood. I checked it out yesterday thinking maybe the power steering pump and instead found that the alternator was about 150 degrees even though we hadn't used the car since the night prior. After consulting Adv. Auto I choose to replace the alternator which I did today and charge the battery to full. (By the way it took about 12-15 hours for the battery to charge to full) So anyways I drove the car out of the garage just to for a test run and the car stalled at low idle. OK I thought. Took it for a 1/2 mile ride and when turning around to come back home the car stalled again. Wife calls me from work to say that it almost stalled again. So the questiopn is could the old regulator on the old alternator have fried my battery? Or maybe there is a short somewhere. I haven't and won't have the chance to run a test on it until tomorrow and when I do how should I proceed with the results of the test?

Tested the battery with the vehicle off. Meter read at 12.5. With the car on 14.5. When I initially start the car it runs through it's high idle sequence and then goes to low idle. Car will idle for about a minute then acts as though it isn't recieveing any fuel, chokes once or twice then dies. Checked the fuse box. Not really anything in there that controls fuel injection. I am thinking that it is some kind of module or sensor that has burned itself when the alternator/regulator crapped out. ?

Wife just called to say that the car will not stay running. It will start, but won't stay running. Although it will if you press on the gas.